Fig. 4
From: Protocol optimization improves the performance of multiplexed RNA imaging
Non-Specific Readout Probe Binding Influences False Positive Rates. (A) mRNA abundance determined via MERFISH versus bulk RNA sequencing for measurements of the colon36. The distribution for the blank barcodes is included (left). (B) mRNA abundance determined via MERFISH from two replicates of the mouse colon36. mRNAs: blue. Blank barcodes: red. (C) Readout usage score (Methods) for all blank barcodes measured in a mouse colon dataset36. Red marks visible outliers. (D-G) Images of mouse colon (D), ileum (E), U-2 OS cells (F), and HEK293 cells (G) stained for DAPI and with the listed readout probes (Table S2). These samples were not stained with encoding probes (Methods). (H) Background binding score for readouts in different tissues. Red: High background. Green: minimal or no detected background. Gray: Not measured. M: mouse. H: human. TG: trigeminal ganglia. For A and B: r represents the Pearson correlation coefficient between the logarithmic expression values. FPKM: Fragments per kilobase per million reads.
